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    SH2D2A SH2 domain containing 2A [ Homo sapiens (human) ]

    Gene ID: 9047, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SH2D2Aprovided by HGNC
    Official Full Name
    SH2 domain containing 2Aprovided by HGNC
    Primary source
    HGNC:HGNC:10821
    See related
    Ensembl:ENSG00000027869 MIM:604514; AllianceGenome:HGNC:10821
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SCAP; TSAD; VRAP; F2771
    Summary
    This gene encodes an adaptor protein thought to function in T-cell signal transduction. A related protein in mouse is responsible for the activation of lymphocyte-specific protein-tyrosine kinase and functions in downstream signaling. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]
    Expression
    Broad expression in appendix (RPKM 5.2), lymph node (RPKM 3.5) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SH2D2A in Genome Data Viewer
    Location:
    1q23.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (156806243..156816848, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155943096..155953700, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (156776035..156786640, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:156711011-156711988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1878 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156717051-156717748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156717749-156718446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156718447-156719143 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156721068-156721842 Neighboring gene mitochondrial ribosomal protein L24 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156729657-156730190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156730191-156730723 Neighboring gene heparin binding growth factor Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156736100-156736726 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:156736727-156737352 Neighboring gene proline rich mitotic checkpoint control factor Neighboring gene Sharpr-MPRA regulatory region 3718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156774267-156774768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156778787-156779288 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156783176-156783722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1438 Neighboring gene neurotrophic receptor tyrosine kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1883 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156808560-156809060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156811133-156811814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156811815-156812494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156814249-156814884 Neighboring gene Sharpr-MPRA regulatory region 5756 Neighboring gene insulin receptor related receptor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1885 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156830955-156831498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156836581-156837238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156844837-156845734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156862813-156863317 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:156865761-156866960 Neighboring gene platelet endothelial aggregation receptor 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Downregulation of lncRNA XIST may promote Th17 differentiation through KDM6A-TSAd pathway in neuromyelitis optica spectrum disorders.
      Title: Downregulation of lncRNA XIST may promote Th17 differentiation through KDM6A-TSAd pathway in neuromyelitis optica spectrum disorders.
    2. TSAd Plays a Major Role in Myo9b-Mediated Suppression of Malignant Pleural Effusion by Regulating TH1/TH17 Cell Response.
      Title: TSAd Plays a Major Role in Myo9b-Mediated Suppression of Malignant Pleural Effusion by Regulating T(H)1/T(H)17 Cell Response.
    3. The ITK SH3 and LCK SH3 domains can both competefor and simultaneously bind to adjacent binding sites on TSAD encompassing aa 242-268.
      Title: The SH3 domains of the protein kinases ITK and LCK compete for adjacent sites on T cell-specific adapter protein.
    4. Data indicate that the T cell-specific adaptor protein (TSAd) SH2 domain interacts with CD6 antigen and linker for activation of T cells protein (LAT) phosphotyrosine (pTyr) peptides.
      Title: CD6 and Linker of Activated T Cells are Potential Interaction Partners for T Cell-Specific Adaptor Protein.
    5. TSAD binds to and co-localizes with Nck. Expression of TSAD increases both Nck-Lck and Nck-SLP-76 interaction in T cells.
      Title: T cell specific adaptor protein (TSAd) promotes interaction of Nck with Lck and SLP-76 in T cells.
    6. The kinase Itk and the adaptor TSAd change the specificity of the kinase Lck in T cells by promoting the phosphorylation of Tyr192.
      Title: The kinase Itk and the adaptor TSAd change the specificity of the kinase Lck in T cells by promoting the phosphorylation of Tyr192.
    7. Data indicate the expression pattern of T cell-specific adapter protein (TSAd) in various healthy lymphoid and non-lymphoid tissues.
      Title: Expression of the T cell-specific adapter protein in human tissues.
    8. in chronic inflammatory demyelinating polyneuropathy we found an association with a homozygous genotype for a low repeat number of tandem GA in the SH2D2A gene
      Title: Polymorphism of CD1 and SH2D2A genes in inflammatory neuropathies.
    9. TSAd, through its interaction with both Itk and Lck, primes Itk for Lck mediated phosphorylation and thereby regulates CXCL12 induced T cell migration and actin cytoskeleton rearrangements
      Title: T cell specific adapter protein (TSAd) interacts with Tec kinase ITK to promote CXCL12 induced migration of human and murine T cells.
    10. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See Variation Viewer (GRCh37.p13)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SH3 domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in angiogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    SH2 domain-containing protein 2A
    Names
    SH2 domain protein 2A
    T cell specific adapter protein TSAd
    T lymphocyte specific adaptor protein
    VEGF receptor-associated protein

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_016849.1 RefSeqGene

      Range
      5001..15606
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001161441.2 → NP_001154913.1  SH2 domain-containing protein 2A isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL158169, AY763099, BQ012931, DB128222
      Consensus CDS
      CCDS53381.1
      UniProtKB/TrEMBL
      Q5UBZ2
      Related
      ENSP00000376123.2, ENST00000392306.2
      Conserved Domains (1) summary
      cl15255
      Location:87 → 198
      SH2; Src homology 2 (SH2) domain

    2. NM_001161442.2 → NP_001154914.1  SH2 domain-containing protein 2A isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, has multiple differences in the coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AF051325, AL158169, DB128222
      Consensus CDS
      CCDS53380.1
      UniProtKB/TrEMBL
      Q5UBZ3
      Related
      ENSP00000357181.3, ENST00000368198.8
      Conserved Domains (1) summary
      cd10416
      Location:69 → 170
      SH2_SH2D2A; Src homology 2 domain found in the SH2 domain containing protein 2A (SH2D2A)

    3. NM_001161443.2 → NP_001154915.1  SH2 domain-containing protein 2A isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, has multiple differences in the coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AL158169, AY763098, BQ012931
      UniProtKB/TrEMBL
      Q5UBZ3
      Conserved Domains (1) summary
      cd10416
      Location:59 → 160
      SH2_SH2D2A; Src homology 2 domain found in the SH2 domain containing protein 2A (SH2D2A)

    4. NM_001161444.2 → NP_001154916.1  SH2 domain-containing protein 2A isoform 2

      See identical proteins and their annotated locations for NP_001154916.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 3' UTR, and coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 2 and 5 encode the same isoform (2).
      Source sequence(s)
      AK222737, DB128222
      Consensus CDS
      CCDS1159.1
      UniProtKB/Swiss-Prot
      O43817, Q5UBZ1, Q5VZS4, Q5VZS5, Q9NP31, Q9UPA7
      UniProtKB/TrEMBL
      B2R9A4
      Conserved Domains (1) summary
      cd10416
      Location:87 → 188
      SH2_SH2D2A; Src homology 2 domain found in the SH2 domain containing protein 2A (SH2D2A)

    5. NM_003975.4 → NP_003966.2  SH2 domain-containing protein 2A isoform 2

      See identical proteins and their annotated locations for NP_003966.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 2 and 5 encode the same isoform (2).
      Source sequence(s)
      AL158169, BC012107, DB128222
      Consensus CDS
      CCDS1159.1
      UniProtKB/Swiss-Prot
      O43817, Q5UBZ1, Q5VZS4, Q5VZS5, Q9NP31, Q9UPA7
      UniProtKB/TrEMBL
      B2R9A4
      Related
      ENSP00000357182.3, ENST00000368199.8
      Conserved Domains (1) summary
      cd10416
      Location:87 → 188
      SH2_SH2D2A; Src homology 2 domain found in the SH2 domain containing protein 2A (SH2D2A)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      156806243..156816848 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433655.1 → XP_047289611.1  SH2 domain-containing protein 2A isoform X7

    2. XM_017002766.2 → XP_016858255.1  SH2 domain-containing protein 2A isoform X5

      UniProtKB/TrEMBL
      Q5UBZ3

    3. XM_017002765.2 → XP_016858254.1  SH2 domain-containing protein 2A isoform X4

      UniProtKB/TrEMBL
      Q5UBZ3

    4. XM_017002764.3 → XP_016858253.1  SH2 domain-containing protein 2A isoform X3

      UniProtKB/TrEMBL
      B2R9A4

    5. XM_006711615.3 → XP_006711678.1  SH2 domain-containing protein 2A isoform X2

      UniProtKB/TrEMBL
      B2R9A4
      Conserved Domains (1) summary
      cd10416
      Location:93 → 194
      SH2_SH2D2A; Src homology 2 domain found in the SH2 domain containing protein 2A (SH2D2A)

    6. XM_017002762.3 → XP_016858251.1  SH2 domain-containing protein 2A isoform X1

      UniProtKB/TrEMBL
      Q5UBZ2

    7. XM_047433652.1 → XP_047289608.1  SH2 domain-containing protein 2A isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      155943096..155953700 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339509.1 → XP_054195484.1  SH2 domain-containing protein 2A isoform X7

    2. XM_054339507.1 → XP_054195482.1  SH2 domain-containing protein 2A isoform X5

    3. XM_054339506.1 → XP_054195481.1  SH2 domain-containing protein 2A isoform X4

    4. XM_054339505.1 → XP_054195480.1  SH2 domain-containing protein 2A isoform X3

    5. XM_054339504.1 → XP_054195479.1  SH2 domain-containing protein 2A isoform X2

    6. XM_054339503.1 → XP_054195478.1  SH2 domain-containing protein 2A isoform X1

    7. XM_054339508.1 → XP_054195483.1  SH2 domain-containing protein 2A isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NP31.3 GenPept UniProtKB/Swiss-Prot:Q9NP31

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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